I would update your source .xml and .php with your changes and make sure you have method=upgrade in the line like this example. and change your <version>to a higher number.
<extension version="3.9" type="plugin" group="content" >
<extension version="3.9" type="plugin" group="content" method="...
If you add the attribute method="upgrade" to the tag extension, your plugin can be installed without uninstalling an earlier version. All existing files will be overwritten, but old files will not be deleted. So you do not need two versions - one for updating and one for new installation!
If you ...